De Novo Assembly and Discovery of Genes That Are Involved in Drought Tolerance in Tibetan Sophora moorcroftiana

Abstract

Sophora moorcroftiana, a Leguminosae shrub species that is restricted to the arid and semi-arid regions of the Qinghai-Tibet Plateau, is an ecologically important foundation species and exhibits substantial drought tolerance in the Plateau. There are no functional genomics resources in public databases for understanding the molecular mechanism underlying the drought tolerance of S. moorcroftiana. Therefore, we performed a large-scale transcriptome sequencing of this species under drought stress using the Illumina sequencing technology. A total of 62,348,602 clean reads were obtained. The assembly of the clean reads resulted in 146,943 transcripts, including 66,026 unigenes. In the assembled sequences, 1534 transcription factors were identified and classified into 23 different common families, and 9040 SSR loci, from di- to hexa-nucleotides, whose repeat number is greater than five, were presented. In addition, we performed a gene expression profiling analysis upon dehydration treatment. The results indicated significant differences in the gene expression profiles among the control, mild stress and severe stress. In total, 4687, 5648 and 5735 genes were identified from the comparison of mild versus control, severe versus control and severe versus mild stress, respectively. Based on the differentially expressed genes, a Gene Ontology annotation analysis indicated many dehydration-relevant categories, including ‘response to water ‘stimulus’ and ‘response to water deprivation’. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways, such as ‘metabolic pathways’ and ‘plant hormone signal transduction’. In addition, the expression patterns of 25 putative genes that are involved in drought tolerance resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The globally sequenced genes covered a considerable proportion of the S. moorcroftiana transcriptome, and the expression results may be useful to further extend the knowledge on the drought tolerance of this plant species that survives under Plateau conditions.

Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae

“…3), suggesting that CYP719A homologs in these high-elevation species might be released from purifying selection and/or there was more positive selection in species occurring at high elevations. It is natural to speculate that such positive selection on a member of the cytochrome P450 gene family (Nelson 2006) might be associated with their known functions for adaptation to high-elevation environments, including drought tolerance and oxygen binding (Bailey-Serres & Chang 2005;Li et al 2015). Overall, our finding that high-elevation species of Dysosma experienced positive selection at CYP719A gene is consistent with preliminary molecular phylogenetic evidence (Mao R.U., unpubl. data) suggesting that the three high-elevation species (D. aurantiocaulis, D. tsayuensis and D. veitchii) evolved from a low-elevation ancestral stock, most likely resembling extant D. versipellis.…”

“…It is natural to speculate that such positive selection on a member of the cytochrome P450 gene family (Nelson ) might be associated with their known functions for adaptation to high‐elevation environments, including drought tolerance and oxygen binding (Bailey‐Serres & Chang ; Li et al . ). Overall, our finding that high‐elevation species of Dysosma experienced positive selection at CYP719A gene is consistent with preliminary molecular phylogenetic evidence (Mao R.U., unpubl.…”

De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress

“…AG/CT and AAG/CTT were the most frequent dinucleotide and trinucleotide SSRs. Similarly, these two types SSRs were also the most frequent di- and tri-nucleotide SSRs identified in Sophora moorcroftiana [15], Heveabra siliensis [16], Capsicum annuum [17], and Sesamum indicum [18], which belong to different orders in the higher plant kingdom. This indicates that these two types SSRs may be somewhat evolutionary conserved in the higher plant kingdom, which is interesting and points to the need for further research.…”

Unigene-based RNA-seq provides insights on drought stress responses in Marsdenia tenacissima

“…It can be used to monitor gene function at the entire genome level in a species without any available genome information . RNA-seq technology has been used to dissect the molecular responses of plant drought tolerance in many plants, especially in non-model plants without available genome information, and some new drought stress genes have been identified (Yates et al, 2014;Wu et al, 2014;Li et al, 2015;Bhardwaj et al, 2015;Fu et al, 2016;Li et al, 2016). Although gene microarray and RNA-seq technology have led to major advances in understanding plant responses to drought, knowledge about the molecular mechanisms underlying drought tolerance in medicinal plants is still extremely limited.…”